A vote on the 20p in the pound offer will be taken at a creditors meeting on June 17 and HMRC - who claim they are owed £35million - will seek a better offer.
A statement from HMRC said: "HMRC is determined to achieve a fair deal for the taxpayer."
The opposition from HMRC would seriously threaten Portsmouth's chances of securing a company voluntary arrangement (CVA) which would enable them to come out of administration and avoid any further points deductions next season.
The club needs 75% of creditors to vote in favour of the 20p deal and Portsmouth's administrator Andrew Andronikou claims that HMRC only hold 21% of the vote.
Andronikou said: "I have heard nothing formal about HMRC's voting intentions.
"According to my calculations they would not be able to block the deal - we are working with all the creditors to achieve the best result for everybody."
Andronikou believes the HMRC should only be claiming £21million and that the other £14million relates to image rights and is challengeable, and that on that basis they would not be able to block the CVA deal.
HMRC have not completely ruled out voting in favour of the deal - but they would need to be convinced that it remains the only possible option to recoup some funds for the taxpayer.
As things stand, they believe they can get some more money back from the club.